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GitHub flow #349

Merged
merged 35 commits into from
Nov 17, 2023
Merged

GitHub flow #349

merged 35 commits into from
Nov 17, 2023

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ddsjoberg
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Thank you for your Pull Request! We have developed this task checklist from the Development Process Guide to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.

Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the devel branch until you have checked off each task.

  • Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
  • Code is formatted according to the tidyverse style guide. Run styler::style_file() to style R and Rmd files
  • Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See Unit Test Guide
  • If you removed/replaced any function and/or function parameters, did you fully follow the deprecation guidance?
  • Update to all relevant roxygen headers and examples, including keywords and families. Refer to the categorization of functions to tag appropriate keyword/family.
  • Run devtools::document() so all .Rd files in the man folder and the NAMESPACE file in the project root are updated appropriately
  • Address any updates needed for vignettes and/or templates
  • Update NEWS.md under the header # admiral (development version) if the changes pertain to a user-facing function (i.e. it has an @export tag) or documentation aimed at users (rather than developers)
  • Build admiral site pkgdown::build_site() and check that all affected examples are displayed correctly and that all new functions occur on the "Reference" page.
  • Address or fix all lintr warnings and errors - lintr::lint_package()
  • Run R CMD check locally and address all errors and warnings - devtools::check()
  • Link the issue in the Development Section on the right hand side.
  • Address all merge conflicts and resolve appropriately
  • Pat yourself on the back for a job well done! Much love to your accomplishment!

Zelos Zhu and others added 25 commits June 12, 2023 19:44
docs: #283 update description and news
07bfe36
@zdz2101
Merge branch 'main' into 283_news_description_postrelease_tidying@devel
71b06b3
@bms63
Merge pull request #284 from pharmaverse/283_news_description_postrel…
8af2f65 
…ease_tidying@devel

Closes #283 update description and news as post-release cleanup tasks
@bms63 @zdz2101
closes #286 commit messaging, new r-cmd vignette (#291)
bd240ad 
* docs: #286 commit messaging, new r-cmd vignette

* chore: #286 spelling

* docs: #286 squash and merge blurb

* Update vignettes/git_usage.Rmd

Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>

* chore: #286 news update

---------

Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>
@zdz2101 @bms63
Closes #271, #213, #260, #240 Documentation Update of get_datasets();…
962b9da 
… keep_source_vars argument; @family tag; compute_ functions (#287)

* docs: #271 #213 clarify get_datasets and add keep_source_vars to prog strat

* docs: #260 cleanup @family mentions

* docs: #240 add blurb about compute functions

* docs: #271 #213 #240 #260 add news blurb

* adopt suggestion for family/keywords

Co-authored-by: Ben Straub <ben.x.straub@gsk.com>

* docs #271 adopt get_dataset feedback

* docs: #213 #240 adopt recommendations from PR

* chore: #240 add BMI to WORDLIST for spellcheck

* chore: #271 #213 #260 adopt feedback

---------

Co-authored-by: Zelos Zhu <zdz2101@github.com>
Co-authored-by: Ben Straub <ben.x.straub@gsk.com>
@zdz2101
Closes #264, #288 cleanup assertions and continue deprecation process (…
80dcf7f 
…#289)

* feat: #288 cleanup deprecation process

* feat: #264 deprecate assert_function

* test: #264 cleanup some tests in assert_function, confused how others would go

* test: #264 rewrite tests in a more logical way

* chore: #264 run styler/lintr

* chore: #288 revert back to devel test file

* chore: #288 properly fix assert_order_vars again

* feat: #264 begin deprecation of redundant assertions

* feat: #288 deprecate assert_named_exprs

* deprecate assert_has_variables properly #264

* chore: #264 run styler

* docs: #264 add blurb in news for the deprecated assertions

* chore: #264 fix description version and remove deprecated examples

---------

Co-authored-by: Zelos Zhu <zdz2101@github.com>
@pharmaverse-bot @dgrassellyb
Propagate renv.lock from pharmaverse/admiralci (#294)
d218980 
renv update from pharmaverse/admiralci

Co-authored-by: dgrassellyb <dgrassellyb@users.noreply.github.com>
@zdz2101
Closes #22 #181 #201 #292 #298 Variety of small-scale general documen…
4f9d68b 
…tation updates (#303)

* feat: #22 add documentation to friendly_type_of

* feat: #181 add the appropriate URL

* feat: #201 #292 add documentation about PR guidance and codeowners

* chore: update wordlist for codeowners

* chore: add NEWS

---------

Co-authored-by: Zelos Zhu <zdz2101@github.com>
@ddsjoberg
Closes #302 Adding Snapshot testing guidance to unit testing vignette (…
4f6350e 
…#308)

* Update unit_test_guidance.Rmd

* Update NEWS.md

* Update NEWS.md
@manciniedoardo
Closes #301: (#307)
c8eec9e 
* #301: edoardo added as author, and author/contributor distinction implemented as in core admiral package

* #301 chore: document
@pharmaverse-bot @galachad
Propagate renv.lock from pharmaverse/admiralci (#310)
64c6618 
* renv / codespaces update from pharmaverse/admiralci

---------

Co-authored-by: galachad <galachad@users.noreply.github.com>
Co-authored-by: Adam Foryś <adam.forys@gmail.com>
@manciniedoardo @rossfarrugia
Closes #295 template documentation@devel (#300)
44f53cd 
* #295 set up package extension guidance page

* #295 fix vignetteindexentry

* #295 chore: spellcheck

* #295 chore: fix encoding issues in vignettes that prevented package from being built

* #295: updates following review

* #295 Chore: spellcheck

* Update vignettes/package_extensions.Rmd

Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com>

* #295 update to refer to admiraldev devel site

* #295 Chore: spellcheck

---------

Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com>
@sophie-gem
Closes #296 document_missing_value_s@devel (#311)
341863b 
* #296 - `missing_value` and `missing_values` added to the table of common arguments.

* #296 - add in discussion of when to use singular vs plural arguments to programming strategy.

* #296 - run checks required for PR and update NEWS.md.

* #296 - Update according to requested changes.

* #296 - revert the 'wrapped' changes in the programming strategy vignette

* #296 - re-insert the new text into the programming strategy vignette, altered according to changes requested.

* #296 - update NEWS.md with changes requested and run the required checks for PR.
@kaz462 @manciniedoardo
Closes #282: Test Data Guidance vignette (#293)
cd6ffc2 
* #282: add test_data_guidance.Rmd, copy from admiraldata README devel

* #282: update .yml

* #282: add link for packages, remove SDTM, add naming conventions for program name

* #282 spelling

* #282: link to two data packages

* #282: updated wordlist

* #282: update pharmaverseadam description

---------

Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com>
@pharmaverse-bot @galachad
Propagate renv.lock from pharmaverse/admiralci (#314)
3e96248 
renv / codespaces update from pharmaverse/admiralci

Co-authored-by: galachad <galachad@users.noreply.github.com>
@pharmaverse-bot @galachad
Propagate renv.lock from pharmaverse/admiralci (#315)
503ffcd 
* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

---------

Co-authored-by: galachad <galachad@users.noreply.github.com>
@StefanThoma @zdz2101
Closes #306 argument descriptions added to table (#320)
0a278a8 
argument descriptions added to table

Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>
@zdz2101
Closes #316 remove messaging that includes "-" as year not handled (#317
c3d1237 
)

* feat: #316 remove messaging that includes "-" as year not handled

* feat: #316 replace warning message

* chore: #316 fix warning message and typos

* chore: #316 add news blurb

---------

Co-authored-by: Zelos Zhu <zdz2101@github.com>
@zdz2101
Closes #318 #321 Documentation updates around admiral.test, staged de…
e4eca25 
…pendencies, and function arguments (#323)
@cicdguy
Fix hardcoded URL (#326)
390dc59 
Resolves #325
@StefanThoma @zdz2101
Closes #312 breakup wall of text (#319)
6fc9925 
* brick in the wall

* remove special characters from image name

* remove special characters from image name

* replaced iframe with png

* fixed image reference

---------

Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>
@zdz2101 @bms63
Closes #328 add missing news entries (#329)
9cb0a46 
* feat: #295 add missing news entries

* feat: #295 add missing news entries

* fixed it

* feat: add news entry for #306

* chore: #312 missing reference

* chore: fix link that pointed to merged branch and use devel

* Update NEWS.md

---------

Co-authored-by: Zelos Zhu <zdz2101@github.com>
Co-authored-by: Ben Straub <ben.x.straub@gsk.com>
@ddsjoberg
GitFlow Migration
9ce44a8
@ddsjoberg
rename to match repo/pkg name
6aa6e41
@ddsjoberg
Merge commit '4dd511e990a553ef16681196cb5a3248d48dff92'
4f0aa71
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Code Coverage

Package Line Rate Health
admiraldev 96% ✔
Summary 96% (1047 / 1093) ✔

@ddsjoberg ddsjoberg marked this pull request as ready for review November 15, 2023 16:43
@ddsjoberg ddsjoberg requested a review from bms63 November 15, 2023 16:47
@ddsjoberg ddsjoberg requested a review from bundfussr November 15, 2023 16:47
bms63
bms63 reviewed Nov 16, 2023
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This one is being removed in another PR as we condensed it into the Contribution model vignette over in admiral

@bms63
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bms63 commented Nov 16, 2023

updated some of the images for git and GitHub usage and removed a few more references to devel. I'll make another pass at this tomorrow.

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bms63 commented Nov 17, 2023

I updated some of the images and removed a few things. The release strategy still needs some work, but I think we can do that in a separate PR.

@ddsjoberg @bundfussr are you both happy in this instant of time? so much coffee today...

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Looks good!

@bms63 bms63 merged commit 76fee62 into main Nov 17, 2023
14 of 16 checks passed
@bms63 bms63 deleted the github-flow branch November 17, 2023 18:10
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9 participants
@ddsjoberg @bms63 @zdz2101 @pharmaverse-bot @manciniedoardo @sophie-gem @kaz462 @StefanThoma @cicdguy